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Yesterday evening, Nintendo graced our 3ds consoles with update 10.4, leaving everyone in the homebrew community freaking out and in complete chaos. So I decided to create this post to list exactly what has been "fixed" by Nintendo to make the system more "stable".
This list is being compiled as a single source from the multitude of other posts in order to bring them all into one place (mostly from replies from this thread: http://gbatemp.net/threads/new-update.410953/)

UPDATE:
Browserhax and Menuhax were just updated, and both now fully work on 10.4 for old and new 3ds.

What has been confirmed:

Memchunkhax2, the kernel exploit used mostly for downgrading and to install legit CIAs, has been patched

APT:IsTitleAllowed has titles and versions hardcoded into NS system module, meaning they won't be able to block any more game save entry points without another system update (Steveice10)

Currently unconfirmed:

Status of Menuhax for Old 3ds

Status of Smashhax

Please let me know if you are either able to confirm/deny any info, or have new info to add to the list.

At this point it seems the best course of action is to stay on 10.3, downgrade to 9.2 and install CFW with emuNAND, which you can safely update to 10.4 on Old 3ds, and some emuNANDs on New 3ds

If you are using oot3dhax, update your payload BEFORE upgrading
This can be done by running HBL and using the oot3dhax installer, and choosing the firmware you will upgrade to. Do this before you upgrade firmware, as not doing so may leave you with no way to upgrade your payload (or at least no easy way to do so)

looks like nintendo snuck in some exploit mitigation in 10.4, in the form of limited physical layout randomization for certain titles

So basically Ninty is now trying to fix the exploitability of the system. So far it doesn't affect a whole lot, but that doesn't mean they will never add more "stability" to the system. For now stay away from 10.4 if you can. (Thanks Joesphvb10 for notifying me about the tweets)

F.A.Q.
Q: How can I update my oot3dhax payload?A: If you still have access to HBL, simply run the oot3d sploit installer and select the appropriate firmware. If you don't have access, you'll have to build a save file and use a USB Save Dongle to put it onto the cartridge. Typically, if you previously had the exploit running on oot3d, you want to update the payload BEFORE upgrading your firmware.

Q: How do I build the save file for oot3d?A: Can't help you there. Either try to follow the instructions on this page, or try to find someone who already built it and posted it online. You can also try to find a friend who hasn't updated, and go from there.

Q: How can I downgrade from 10.4?A: You can't. The kernel exploit used from 9.3-10.3 to downgrade firmware (memchunkhax2) was patched as of 10.4. So for now it is impossible. This also makes it impossible to install legit cia files.

Pretty much, in 10.4, they've made it where if ironfall is on 1.0 or 1.1, then it forces you to update to the latest, effectively removing ironfall from homebrew access as of 10.4, anything prior shouldn't cause this i don't believe.

Pretty much, in 10.4, they've made it where if ironfall is on 1.0 or 1.1, then it forces you to update to the latest, effectively removing ironfall from homebrew access as of 10.4, anything prior shouldn't cause this i don't believe.

Click to expand...

It's only enforced in 10.4, and it's only for Ironfall.
So if you are on 10.3, you can still use Ironhax, and if you are on 10.4 it will not affect any other installed item (at least for now)